Titan PE human read removal step

[k-florek]

Inclusion of a Task to remove human reads is needed to prepare fastq files for upload into SRA. The ideal choice is to use the NCBI SRA Human Scrubber tool.

Process for this issues should be:

• Pick the approach/tool to be used
  • NCBI SRA Human Scrubber makes the most sense but is still in "testing"
• Containerization (Docker) of tool and added to StaPH-B/docker-builds
  • Optionally use an already built container
• Develop WDL task and include in Titan PE workflow
  • Raw fastq reads should still have fastqc performed
  • Reads with human reads removed should be used for all downstream steps in Titan PE

[kevinlibuit]

Issue in NCBI scrubber identified; output incompatible with downstream tasks

*edit hyperlink

[kevinlibuit]

Issue with the NCBI Scrubber identified and addressed in latest docker release: ncbi/sra-human-scrubber:1.0.2021-04-19 We incorporated the updated tool into a two tasks (pe/se) and incorporated these into our Titan Illumina PE, ONT, and ClearLabs workflows--the scrubber is not yet compatible with short-read data expected for the Titan Illumina SE workflow.

[kevinlibuit]

Issue closed in Theiagen repo with latest PR: https://github.com/theiagen/public_health_viral_genomics/pull/10